At the turn of the 20th century, Mary Lennox is a neglected and unloved 10-year-old girl, born in British India to wealthy British parents who never wanted her and made an effort to ignore her. She is cared for primarily by native servants, which spoils her and allows her to have full reign. After a cholera epidemic kills Mary's parents, the few surviving servants flee the house without Mary.
She is discovered by British soldiers who place her in the temporary care of an English clergyman, whose children taunt her by calling her "Mistress Mary, quite contrary". She is soon sent to England to live with her uncle, Archibald Craven, whom her father's sister Lilias married. He lives on the Yorkshire Moors in a large English country house, Misselthwaite Manor. When escorted to Misselthwaite by the housekeeper Mrs. Medlock, she discovers Lilias Craven is dead and that Mr. Craven is a hunchback.
At first, Mary is as angry and contrary as she was before she was sent there. She dislikes her new home, the people living in it and, most of all, the bleak moor on which it sits. Over time, she becomes more spirited and less cantankerous and befriends her maid, Martha Sowerby, who tells Mary about Lilias Craven, who would spend hours in a private walled garden growing roses. Lilias Craven died after an accident in the garden ten years prior, and the devastated Archibald locked the garden and buried the key.
Mary becomes interested in finding the secret hidden garden herself, and her ill manners begin to soften as a result. Soon, she comes to enjoy the company of Martha, the gardener Ben Weatherstaff, and a friendly robin redbreast. Her health and attitude improve with the bracing Yorkshire air, and she grows stronger as she explores the estate gardens. Mary wonders about the secret garden and about mysterious cries that echo through the house at night.
As Mary explores the gardens, the robin draws her attention to an area of disturbed soil. Here, Mary finds the key to the locked garden, and eventually discovers the door to the garden. She asks Martha for garden tools, which Martha sends with Dickon, her 12-year-old brother, who spends most of his time out on the moors. Mary and Dickon take a liking to each other, as Dickon has a kind way with animals and a good nature. Eager to absorb his gardening knowledge, Mary tells him about the secret garden.
One night, Mary hears the cries once more and decides to follow them through the house. She is startled to find a boy of her age named Colin, who lives in a hidden bedroom. She soon discovers that they are cousins—Colin being the son of Archibald Craven—and that he suffers from fevers and an unspecified spinal condition which precludes him from walking and causes him to be confined to bed. He, like Mary, has grown very spoiled, with servants obeying his every whim in order to prevent the frightening hysterical temper tantrums into which Colin occasionally flies. Mary visits him every day that week, distracting him from his troubles and despondency with stories of the moor, Dickon and his animals, and the secret garden. Mary eventually confides to Colin that she has access to the secret garden, and he asks to see it. Colin is put into his wheelchair and brought outside into the secret garden. It is the first time he has been outdoors for several years. With Mary and Dickon's help and encouragement, and absorbing the beneficial effects of the growing garden, he begins to open up to the world around him and finds renewed hope for his future.
While in the garden, the children look up to see Ben Weatherstaff looking over the wall on a ladder. Startled to find the children in the secret garden, he admits that he believed Colin to be "a cripple." Angry at being called "crippled," Colin rises shakily from his chair and finds that he can stand on his legs, albeit they are weak from long disuse. Mary and Dickon spend almost every day in the garden with Colin, and continue to encourage him to grow stronger and attempt walking. Together, the children and Ben conspire to keep Colin's recovering health a secret from the other staff to surprise his father, who is travelling abroad.
While his son's health improves, Archibald experiences a coinciding increase in spirits, culminating in a dream where his late wife calls to him from inside the garden. When he receives a letter from Mrs. Sowerby, who advises him to come back to Misselthwaite, he takes the opportunity to finally return home. He walks the outer garden wall in his wife's memory, and hears voices inside. He finds the door unlocked and is shocked to see the garden in full bloom and his son restored to health, having just won a race against Mary. The children tell him the entire story, explaining the restoration of both the garden and Colin. Archibald and Colin then walk back to the manor together, observed by the stunned and incredulous servants.
